Yes, agreed, NCCI is not universal, nor is it required to be, and many commercial payers do use different bundling methodologies.
One thing to keep in mind is that NCCI, in spite of the fact that two of letters stand for 'correct coding', is not a coding guideline - it is a reimbursement policy. It is directly tied to the way that Medicare calculates their payment rates for particular procedures. These bundling rules are based on what Medicare includes or does not include in the rate that they set for any given procedure. Private payers may calculate their rates differently, and so their bundling rules can also be different. Unfortunately, unlike Medicare which is required by law to publish their rules for transparency, private payers are not under obligation to do so, and the bundling rules such as McKesson's will often be proprietary and not readily available for everyone to see.
If your practice is contracted with the payer, then there almost certainly is a clause in your contract that says that you have agreed to accept those rules, so it will likely be difficult to challenge these edits. But I always advise that if you are finding that a particular payer's reimbursement policy is negatively affecting your provider because a particular procedure that you perform often is being underpaid or denied due to one of their rules, this is something you should track and bring to the table when your contract is up for negotiation and ask that you be compensated for it with a higher payment rate for the practice to offset these losses.